I think that I found it: Switching the 'restart_mode' from 'restart' to
'from_scratch' in the name list '&control' "released" the atoms to relax
properly.
I have no idea why this should have an effect on the relaxation: I
always keep it as 'restart' in the calculations with the NEB, and the code
'pw.x' performs the restart if the files needed for a restart are present,
otherwise the calculation starts from the given configuration and with the
same initialisation of the electronic structure as with 'from_scratch', so
I was expecting the same to happen with the NEB. My mistake, "never expect
the logic of the developer to be the same as your own". Now happily
computing all kinds of barriers and paths! :)
Greetings from Paris and Grazie a Giuseppe again,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / [email protected] / http://www.iki.fi/~apsi/
Слава Україні
On Thu, 27 Apr 2023, Ari P Seitsonen wrote:
Dear Giuseppe,
Thank you for the comment. One of my concerns was that the energy in the
images does not really change:
grep -w ' 4 ' neb.out
4 -78481.6171806 29.739170 F
4 -78481.6171811 29.738137 F
4 -78481.6171811 29.736993 F
4 -78481.6171811 29.734436 F
4 -78481.6171812 29.727381 F
4 -78481.6171809 29.718296 F
4 -78481.6171808 29.712880 F
4 -78481.6171810 29.713046 F
4 -78481.6171810 29.719086 F
4 -78481.6171811 29.729326 F
4 -78481.6171812 29.740800 F
4 -78481.6171805 29.752151 F
4 -78481.6171812 29.761356 F
4 -78481.6171812 29.769083 F
4 -78481.6171805 29.774024 F
4 -78481.6171812 29.776518 F
4 -78481.6171800 29.776688 F
4 -78481.6171811 29.773882 F
There are forces on the atoms, here again on one of them on the fourth image:
atom 84 type 2 force = -0.00407872 0.00078289 -0.00018719
atom 84 type 2 force = -0.00407494 0.00078224 -0.00018711
atom 84 type 2 force = -0.00407554 0.00078237 -0.00018713
atom 84 type 2 force = -0.00407560 0.00078248 -0.00018709
atom 84 type 2 force = -0.00407511 0.00078229 -0.00018712
atom 84 type 2 force = -0.00407619 0.00078255 -0.00018726
atom 84 type 2 force = -0.00407623 0.00078272 -0.00018718
atom 84 type 2 force = -0.00407528 0.00078225 -0.00018721
atom 84 type 2 force = -0.00407564 0.00078257 -0.00018705
atom 84 type 2 force = -0.00407500 0.00078222 -0.00018713
atom 84 type 2 force = -0.00407577 0.00078249 -0.00018711
atom 84 type 2 force = -0.00406905 0.00078120 -0.00018643
atom 84 type 2 force = -0.00407551 0.00078243 -0.00018722
atom 84 type 2 force = -0.00407271 0.00078203 -0.00018711
atom 84 type 2 force = -0.00407796 0.00078294 -0.00018727
atom 84 type 2 force = -0.00407607 0.00078266 -0.00018716
atom 84 type 2 force = -0.00407437 0.00078207 -0.00018715
atom 84 type 2 force = -0.00407642 0.00078274 -0.00018719
The 'path length' indeed keeps on increasing - what is this, if the energies
of the images remain the same?
initial path length = 5.0000 bohr
path length = 5.000 bohr
path length = 5.000 bohr
path length = 5.003 bohr
path length = 5.013 bohr
path length = 5.094 bohr
path length = 5.337 bohr
path length = 5.702 bohr
path length = 6.163 bohr
path length = 6.695 bohr
path length = 7.277 bohr
path length = 7.897 bohr
path length = 8.546 bohr
path length = 9.216 bohr
path length = 9.904 bohr
path length = 10.606 bohr
path length = 11.321 bohr
path length = 12.047 bohr
path length = 12.783 bohr
Probably I am doing something really stupid somewhere... I will try to look
at the source code next and try to understand somewhat better for what is
done in the code, the meaning of the variables and so on.
Greetings,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / [email protected] / http://www.iki.fi/~apsi/
Слава Україні
On Thu, 27 Apr 2023, Giuseppe Mattioli wrote:
Dear Ari
The NEB is not exactly "stuck"
path length = 8.546 bohr
path length = 9.216 bohr
path length = 9.904 bohr
The MEP length keeps increasing. Maybe a look into the trajectory files can
tell you what's happening. If any other source of misbehavior can be
excluded, try to go ahead (maybe fixing the position of "useless" atoms).
I've experienced NEB in large systems converged after several hundreds
steps.
HTH
Giuseppe
Quoting Ari P Seitsonen <[email protected]>:
Dear Users,
I have a problem in the calculations with the method NEB: The atoms do
not get relaxed even if there are clearly forces on the atoms. The
electronic structure converges well, and the relaxation of the ions
follows nicely when the NEB is not used.
I have in the input
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'restart'
string_method = 'neb'
nstep_path = 30
ds = 0.2
opt_scheme = "broyden"
num_of_images = 8
k_max = 0.3
k_min = 0.2
CI_scheme = "auto"
! minimum_image = .true.
first_last_opt = .true.
path_thr = 0.1
/
END_PATH_INPUT
and
&ions
/
I have tried with different values of 'num_of_images', 'k_min' and
'k_max', with the climbing image and without. One calculation - a
diffusion path of one ad-atom on a surface - worked well, all other become
stuck with the output like:
------------------------------ iteration 12
------------------------------
cpu = 0 tcpu = 9589.5 self-consistency for image 1
cpu = 0 tcpu = 9656.9 self-consistency for image 3
cpu = 0 tcpu = 9823.9 self-consistency for image 5
cpu = 0 tcpu = 10043.8 self-consistency for image 7
activation energy (->) = 10.012055 eV
activation energy (<-) = 6.833374 eV
image energy (eV) error (eV/A) frozen
1 -78491.5920678 0.000987 F
2 -78490.3334035 7.018378 F
3 -78486.4101831 18.058881 F
4 -78481.6171805 29.752151 F
5 -78481.5800131 29.996389 F
6 -78485.0169815 13.489042 F
7 -78487.7020649 7.675245 F
8 -78488.4133872 8.072137 F
climbing image = 5
path length = 8.546 bohr
inter-image distance = 1.221 bohr
------------------------------ iteration 13
------------------------------
cpu = 0 tcpu = 10165.0 self-consistency for image 1
cpu = 0 tcpu = 10267.1 self-consistency for image 3
cpu = 0 tcpu = 10487.8 self-consistency for image 5
cpu = 0 tcpu = 10710.2 self-consistency for image 7
activation energy (->) = 10.011390 eV
activation energy (<-) = 6.833374 eV
image energy (eV) error (eV/A) frozen
1 -78491.5914028 0.000493 F
2 -78490.3334036 7.099250 F
3 -78486.4101837 17.820470 F
4 -78481.6171812 29.761356 F
5 -78481.5800130 29.998875 F
6 -78485.0169810 13.636010 F
7 -78487.7020648 7.675132 F
8 -78488.4133870 8.071850 F
climbing image = 5
path length = 9.216 bohr
inter-image distance = 1.317 bohr
------------------------------ iteration 14
------------------------------
cpu = 0 tcpu = 10843.3 self-consistency for image 1
cpu = 0 tcpu = 10962.6 self-consistency for image 3
cpu = 0 tcpu = 11183.6 self-consistency for image 5
cpu = 0 tcpu = 11420.4 self-consistency for image 7
activation energy (->) = 10.011390 eV
activation energy (<-) = 6.833374 eV
image energy (eV) error (eV/A) frozen
1 -78491.5914032 0.000582 F
2 -78490.3334034 7.139704 F
3 -78486.4101836 17.548234 F
4 -78481.6171812 29.769083 F
5 -78481.5800132 29.998295 F
6 -78485.0169814 13.849319 F
7 -78487.7020642 7.669197 F
8 -78488.4133871 8.072137 F
climbing image = 5
path length = 9.904 bohr
inter-image distance = 1.415 bohr
------------------------------ iteration 15
------------------------------
...
So the atoms do not move, the electronic structure is converged in few
iterations, but the energies of individual images change in the micro-eVs.
Any idea would be appreciated; thank you in advance for any hints.
Greetings,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / [email protected] / http://www.iki.fi/~apsi/
Слава Україні
GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <[email protected]>
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effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
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_______________________________________________
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_______________________________________________
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list [email protected]
https://lists.quantum-espresso.org/mailman/listinfo/users
